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Functional microexons have not previously been described in filamentous fungi. Here, we describe a novel mechanism of transcriptional regulation in <i>Trichoderma</i> requiring the inclusion of a microexon from the <i>Xlr2</i> gene. In low-glucose environments, a long mRNA including the microexon encodes a protein with a GAL4-like DNA-binding domain (Xlr2-α), whereas in high-glucose environments, a short mRNA that is produced encodes a protein lacking this DNA-binding domain (Xlr2-β). Interestingly, the protein isoforms differ in their impact on cellulase and xylanase activity. Deleting the <i>Xlr2</i> gene reduced both xylanase and cellulase activity and growth on different carbon sources, such as carboxymethylcellulose, xylan, glucose, and arabinose. The overexpression of either <i>Xlr2-α</i> or <i>Xlr2-β</i> in <i>T. virens</i> showed that the short isoform (Xlr2-β) caused higher xylanase activity than the wild types or the long isoform (Xlr2-α). Conversely, cellulase activity did not increase when overexpressing <i>Xlr2-β</i> but was increased with the overexpression of <i>Xlr2-α</i>. This is the first report of a novel transcriptional regulation mechanism of plant-cell-wall-degrading enzyme activity in <i>T. virens.</i> This involves the differential expression of a microexon from a gene encoding a transcriptional regulator.